### This script will create .sh files that will batch out a moving window average of AWAP preds based on year
# Directory for .sh files

tmp.pbs = '/home1/99/jc152199/tmp.pbs1/'
setwd(tmp.pbs)

### Out directory

out.dir = '//home1/99/jc152199/MicroclimateStatisticalDownscale/5kASCII/AWAP7daymovavg/'

# Location of script to run

script.file = paste(out.dir,'MovingWindow2run.r',sep='')

### Use a for loop to create an .sh file for each year between 1976 and 2005

for (yearx in c(1976:2005))

	{
	
	# Create a name for the .sh file
	
	tname = paste(yearx,'.sh',sep='') # Create a name for the .sh script
	
	# Define some arguments
	
	arg.yearx = paste('yearx="',yearx,'" ',sep='') # Define the argument for yearx
				
	zz = file(tname,'w') # This command creates a file with the name 'tname' The 'w' command opens the file and writes the following lines of text into it
		
		cat('##################################\n',file=zz) # First blank line of .sh file ### Note the use of '\n', any text following this will be on the next line
		cat('#!/bin/sh\n',file=zz) # First command line for HPC
		cat('cd $PBS_O_WORKDIR\n',file=zz) # Sets the directory to write out summary files at the above directory 'tmp.pbs'
		cat("R CMD BATCH --no-save --no-restore '--args ",arg.yearx,"' ",script.file,' ',gsub('.sh','',tname),'.Rout \n',sep='',file=zz) # This line tells R not to save to the .Rdata file and also not to restore the environment from the .Rdata file, very important when batching or you will get multiple fuckups, also defines the arguments, says where script to run is located, and defines the name for the R.out file
		cat('##################################\n',file=zz) # Last blank line of .sh file
				
	close(zz) # Closes the .sh file that you've just written
	
	cat('\n',tname)
	
	# The follow line submits the job to the HPC, leave it commented out until you're ready to RUN all the jobs\
	# Always run the script first without removing the comment, this will still generate the .sh files for you to check before running
	# Once you're happy with that then submit a single .sh file and make sure it runs through to completion before batching out the rest with the following line
				
	system(paste('qsub -m n -l nodes=1:ppn=8 ',tname,sep=''))
	system(paste('sleep 1'))
							
	}
	
# End Loop